


Secret Son

by skippy_is_invisible



Series: Secret Son [1]
Category: Iron Man (Movies), Marvel Cinematic Universe, Spider-Man (Tom Holland Movies), The Avengers (Marvel Movies)
Genre: Angst, Bisexual Peter Parker, Hurt/Comfort, Parent Tony Stark, Peter Parker Needs a Hug, Peter Parker is Tony Stark's Biological Child, Tony Stark Acting as Peter Parker's Parental Figure, Tony Stark Has A Heart, Trans Peter Parker
Language: English
Status: In-Progress
Published: 2020-11-15
Updated: 2020-11-24
Packaged: 2021-03-10 06:55:00
Rating: Not Rated
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 3,244
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/27579461
Author URL: https://archiveofourown.org/users/skippy_is_invisible/pseuds/skippy_is_invisible
Summary: Peter Stark is a secret. A well kept secret. Only those within Tony Stark's inner circle know about his son. That is, until one day Peter gets kidnapped and his ransom is posted to the internet for the entire world to see. Tony must ask for help from the rogue Avengers to save his son. (This takes place after Civil War and Peter does not have his powers.)
Relationships: Pepper Potts/Tony Stark, Peter Parker & Tony Stark, Tony Stark & Avengers Team
Series: Secret Son [1]
Series URL: https://archiveofourown.org/series/2015939
Comments: 11
Kudos: 85





	1. Chapter 1

**Author's Note:**

> See end for notes

This wasn’t supposed to happen. None of this was supposed to happen... 

Tony panicked as he watched the screen in horror. Streaming live to the entire internet, was his son, Peter, drugged and bound to a chair. With what appeared to be a broken nose with a trail of blood leading down his chin and what looked to be a bruise forming under Peter’s left eye. Off screen, two voices demanded ten billion dollars in exchange for Peter’s life. His worst nightmare had come true.

“You will be given further instructions in the coming hours.” One voice said.

“Do as we say Stark, and your precious son won’t get hurt.” The other said.

Tony felt as if he couldn’t breathe. His son. His son he tried so hard to protect, could die by the hands of strangers and it would be his own fault.

No one outside of Pepper, Happy, Natasha, the Leeds family, and Rhodey, knew that Tony Stark had a child. Originally, Tony didn’t want the media to know he had a child because Tony knew how horrible and stressful it was growing up with a camera constantly being shoved in your face. Not to mention the lack of privacy. After he became Iron Man and joined the Avengers, with the amount of danger they faced, Tony had more reasons to keep his son a secret.

Tony’s legs gave out underneath him. His mind was racing. ‘My fault, my fault, my fault, my fault.’ His worst nightmare became reality. Tony’s memories flashed back to Afganistan, except this time it wasn’t him experiencing the torture. He imagined Peter. Tony was pulled from his thoughts when his phone rang.

“Tony?”

His voice came out as a sob. “Nat!”

“I saw-”

“He’s gone! He’s been taken!”

“I know Tony. You need to calm down so-”

“Calm down?! My baby is missing! You expect me to calm down?!”

“Panicking isn’t going to help find Peter.”

Tony forced himself to take deep breaths. ‘Focus…’ He told himself. ‘Peter… Peter needs me. Get it together… Peter needs you. Breathe.’

Tony counted to three, took another breath, “Okay… Okay…” Tony whispered into the phone. He was still panicking but he forced himself to be functional enough to find his son.

“Good. We’re on our way. Call your family and we’ll be there in a few hours.” Natasha hung up the phone. ‘This is going to be interesting to explain.’ She thought as she made her way to gather the rest of the rogues.  
________________

When Pepper answered her phone she felt dread. She didn’t know why at first, until she heard Tony’s voice. Tears spilled out of the corners of her eyes. She canceled her meetings and told Tony she would be on the first flight back to New York.

Rhodey dropped everything with no explanation to his superiors, to help find his nephew.

Before Tony could call Happy, Midtown High called Tony to inform him that Peter never arrived at school that morning. Tony didn’t know what to say. How do you tell your child’s school that you just found out that they have been kidnapped? All that Tony responded with was an “Okay.” and hung up.

Peter had left home with Happy at 7:30 a.m. School for Peter didn't start until 8:00 a.m. Peter always arrived at 7:45. He would then spend the next ten minutes talking with his friends in the halls on their way to class. Peter would then arrive at his first class by 7:57, three minutes before the bell rang. That was Peter’s routine.

*ACA DECA Dweebs*

Ned: Dude, where are you?

MJ: You better not be sick! I don’t want to have to suffer through Steven’s class by myself! 🤬

Brad: Anyone know where Peter is?

Flash: Parker

Flash: Parker

Flash: Parker!

Flash: Hey DICKHEAD! Answer your phone!!!

Betty: Be nice Flash

Betty: Are you ok? We miss you 💕

Brad: Please tell me you didn’t get food poisoning from the cafeteria again 🤢

Flash: C’mon Parker

Flash: You can’t leave me alone with these losers

MJ: You’re going to miss the Spanish quiz

Ned: Betty and I can get your homework if you’re not showing up today

Ned: Peter?

Ned: Peter?

MJ: Peter?

Tony hacked Peter’s phone to see if he could find anything useful. All that he found was concerned text from his friends and his last known location, which was a block away from Peter’s school. Tony still hadn’t heard from Happy yet. He was furious but also concerned.

__________________

“Hey, Nat?” She found her friends hunched over the kitchen table staring at Sam’s phone.

“Yes, Clint?”

They all turned to look at her. “Does Tony actually have a kid?”

“Yes.”

“You’ve got to be joking.” Sam said. “Stark… A kid?... Really?”

“Yes.”

“How come Tony never told us?” Steve asked. He sounded hurt. “How do you know about him but we don’t.”

“I was never supposed to know, but that’s not important right now. Tony and Peter need our help.”

“Am I coming with you?” Bucky asked. Natasha thought about it for a moment before nodding. It took them less than five minutes to grab their gear and hop on the jet.

Wanda had been unusually quiet once she found out Tony had a kid. Actually, most of them had been pretty quiet. They didn’t ask her any more questions. They knew she wouldn’t tell them much until they met up with Tony. But Wanda stood out. Everyone knew she had a complicated relationship with Tony, they expected more of a reaction from her when they found out about Tony’s son. But she remained quiet with a blank face.

_____________

Peter had an eventful morning to say the least. But it didn't start out that way. He woke up, had breakfast with his dad, got ready and left for school with his uncle Happy. What was out of the ordinary had started when they were on the way to school. There had been a car accident a few blocks from Midtown, causing them to take a different route. Peter would wonder what would have happened if they didn’t go a different route, or if they had left home earlier, would the same thing have happened?

Peter woke up in a dark room tied to a chair. He tried to look around and get a better view of his surroundings but couldn’t see much. All that could be seen was light through the small crack at the bottom of the door. He tried to free his hands but only managed to hurt his wrists. The panic began to set in.

‘Don’t panic.’ Peter thought to himself. He took a couple deep breaths and tried to recall the last thing he could remember. It took a minute but the last thing Peter could remember before waking up was sitting in the car with Happy, chatting about his upcoming history project. Then stopping at a red light… Then the sounds of windows mashing and Happy shouting, everything went black after that.

Peter then began to panic. Realizing that he had been kidnapped, and was alone alone.

‘How do they know I exist!? How do they know who my dad is!?’ Peter’s mind was racing. ‘What did they do to Uncle Happy!? Is Uncle Happy dead?!’

The last thought made Peter sick. He refused to believe that his uncle was dead. ‘There’s a good possibility that he probably is.’ Peter shook his head and tried to push down the panic and the thought his uncle might be dead, but he couldn’t.

As if on cue, two of his abductors walked in and switched on a light. Peter couldn’t make out much of their faces but he could tell that he couldn’t beat them in a fight.

‘Don’t freak out.’ Peter thought. ‘They probably want money… They won’t hurt you until Dad pays them…’

Tony had made Peter learn what to do if Peter was ever abducted. Peter was taught basic self defense and how to respond to certain situations. However, Peter seemed to have forgotten all that information as soon as his abductors spoke to him. He was frozen with fear and couldn’t respond.

“Hey kid!” Peter blinked and looked up at the man. “Pay attention when I’m speaking.”

Peter only nodded.

“So, as I was saying… Your daddy’s rich and we could use some cash. So you're going to help us out.” As the man was talking, Peter couldn’t help but think, ‘This is literally the most stereotypical monologue I’ve ever heard.’

“And our boss has an axe to grind with your father.” The other spoke, “We decided to team up.”

‘So you’re not the master minds.’ Peter thought. “So what we’re gonna do is set up our little webcam and send a message to your dad.” As the one fumbled with the tripod, the other asked, “What was the password to the YouTube account?”

“What?” That got Peter’s attention.

“What do ya mean, what?”

“Are- Are you st-streaming this to You-YouTube?” Peter stuttered out.

“We’re streaming this on every possible platform to get Stark’s attention.”

The shorter man spoke, “I’ll finish setting this up. You make him look nice for the camera.” He said with a smirk

Before Peter could say anything, a fist clocked him right in the nose. He let out a yelp and tears pricked the corner of his eyes. His nose instantly began throbbing as he felt warm liquid drip down his face. When the tall man raised his hand again, Peter turned his head as fast as he could, resulting in what would form to be an ugly bruise under Peter’s left eye.

Before the man could hit him again, his phone started ringing. The man answered his phone, said a few short sentences before hanging up.

“You got everything set up?” He asked his accomplice.

“We’re good to go.”

“Alright kid,” He grabbed a fistful of Peter’s hair. “Smile for the camera.”


	2. Chapter 2

**Notes for the Chapter:**

> See end of chapter for notes

“Friday! Did you find Happy yet?” Tony asked, hunched over his computer trying to contact Fury for the fifth time that day.

“Still working on that boss.” The A.I. responded.

Tony put his head in his hands. Everything felt hopeless. It had been two hours since Tony last heard from Peter’s abductors. Two hours since Tony had proof that his son was still alive.

F.R.I.D.A.Y. interrupted Tony’s thoughts, “Boss, the Avengers have arrived.”

‘Great.’ Tony thought. ‘Another thing to send me spiraling into a panic attack.’

“Boss?”

“What?” Tony snapped.

“Your heart rate has increased significantly. Do you want me to guide you through one of your breathing exercises?”

“No Friday. Let them in.” In walked Steve, Natasha, Clint, Wanda, Sam, and Bucky. Tony’s former friends who he once considered to be family. Tony forced himself to at least look calm. While internally freaking out.

“Boss-” 

“Unless it’s about Peter I don’t want to hear it, Fri.”

Natasha was the first to approach Tony. She pulled him into a hug that he did not reciprocate. Tony just stood there, stiff and emotionless, on the outside anyways.

Natasha pulled away. “What can we do to help.” 

“Find my kid.” Tony responded.

Those three words broke the Avengers. Tony, who was once their friend, stood before them, feeling absolutely helpless. The most important thing in Tony’s world was missing, and they didn’t know if it could bring that back.

“Walk us through what happened.” Clint said. Tony gestured for them to follow him over to his monitors. “We already saw the video but we need to know what happened before that.”

Tony let out a shaky breath. “Everything started off normal this morning…” Tears pricked at the corner of his eyes. Tony pushed his glasses up further. He refused to cry. “Peter got up, I made him breakfast, he got dressed and ready for school. And then…” His voice trailed off.

“What time did he leave for school?” Clint asked.

“7:30.” Natasha answered for him. The rogues gave her a look but she ignored them.

“Did you take him to school?” Steve was glad Clint was taking the lead. Although Tony was once his friend, Steve had no idea how to handle this situation. None of them did.

“No, I had a meeting. Happy drove him.”

“Where is Happy?” Natasha asked.

“He’s missing too… I didn’t even know Peter wasn’t at school until it was broadcast to the entire world.”

“I’m sorry, Tony.” Steve didn’t know how else to respond.

“I tried tracking his phone but that didn’t work, so I sent out drones all over the city and Friday is currently looking at every single security camera in the city.”

“Is there anything you need us to do?” Sam asked.

“Get in contact with Fury.”

“He hasn’t answered?” Clint sounded surprised.

“No! He hasn’t! He has the best resources in the world! I never asked him for anything but the one time I need him he doesn’t pick up!”

“Calm down Tony.” Right as those words left Steve’s mouth he knew it was the wrong thing to say.

“Calm down?! How the hell do you expect me to calm down!?” Tony marched right up to Steve. “My baby is missing and you expect me to calm down!”

“I didn’t mea- I just-”

“What Steve?!” Tony was fuming.

“I don’t know.”

“Yeah, you don’t know! You don’t know what it’s like to be a parent! So keep your damn mouth shut!”

“Boss, I have news.” Friday interrupted.

“What is it?”

“I found Happy, sir.”

“Where is he?”

“He is currently at the hospital being treated for several broken bones and a head injury.”

“What?!”

_____________

After being drugged, Peter woke up a couple hours later. He was still tied to a chair, but at least a small light was still on. Once Peter cleared his head, he tried to get a better look at his surroundings. 

The first thing Peter became aware of was the fact that he didn’t have his brightly colored converse shoes or mismatch socks anymore. And the floor was wet… And Peter could see his breath in the light.

“This is bad. This is very, very bad.” Peter whispered to himself. From a young age Peter had known that there would always be a small possibility that he could be kidnapped. When he first became aware was when Tony had returned from Afghanistan. Peter was still young at the time and didn’t fully understand as to why anyone would want to take him but the look on his father’s face made him realize there was something seriously wrong. Shortly after Tony made Peter train with Happy, and soon Natasha, as to what to do if and when he gets kidnapped, along with self defense. Peter was never a fan of those lessons. He knew they were important but they made him more paranoid than anything. He never even took them that seriously until their house in Malibu was attacked.

“Okay Peter. Focus…” He told himself. “Step one. Escape bindings. Step two, get as far away as possible from wherever here is.” Peter had no idea what he was getting himself into. “Should be easy enough and if I’m lucky I can find my shoes on the way… Yeah great idea.”

___________

“I’m on my way. Tell Pep and Rhodey that I’m at the hospital if they get here before I do.”

“Yes boss.”

“Tony,” Nat stepped in front of him. “You should stay here.”

“Wh-”

“Listen, you’re not thinking clearly and what Happy needs right now is someone who can help him. You’re too anxious.”

“He knows-”

“I’ll go talk to him and bring him back here. And besides, those reporters will hound you as soon as you step outside.”

“She’s right Tony.” Clint said. “The last thing we need is for you to have a nervous breakdown. Or you blowing up at a reporter and having it all over the news.”

“But-”

“You already blew up at Steve. It’s best you try to keep it contained.” 

He dug his nails so deep into his palms he could feel blood start to drip out. Tony hated to admit it but he knew they were right. He could only imagine what the tabloids were printing about his son. Once Pepper got home she could help to keep the media contained for the time being.

“I’ll go with Nat to the hospital. You stay here with them and wait for Rhodes and Pepper to show up ok.”

Tony nodded. 

“And remember they might contact you again with instructions.” 

“Yeah, you’re right.” Tony whispered. Normally Clint would tease Tony for admitting that he was right but that was not the time.

“Don’t do anything stupid.” Natasha said. “Hopefully we’ll be back with answers soon.”

As the rogues left, they seemed to have an unspoken conversation with their eyes. Tony was too preoccupied to notice.

After about thirty minutes giving himself rope burn, Peter managed to free his limbs. He knew he needed to move fast before anyone came to check in on him. He made his way over to the door.

“Of course it’s locked.” Peter sighed. “Why wouldn’t it be.”

The door seemed old. Peter figured his best option was to take a running start and launch his entire body weight at it and hope it opens.

That did not work. However it did alert Peter’s abductors. Seconds later the door swung open and the two men found Peter on the floor. As they took their first steps across the threshold Peter scrambled to his feet and backed away as quickly as he could. Eventually Peter was backed into a corner. He tried to fight back but a single punch to the stomach from the larger of the two men sent him doubling over.

“Teach him a lesson for misbehaving.” A woman’s voice came from the doorway. “He’s crafty like his father.” Peter tried to get a good look at the woman but only caught a glimpse as she turned around. “I’ll get the other restraints. Then let’s send another message to Stark.

__________

“Tony!” Rhodey shouted as he entered the room. Everyone turned to look at him. He ignored them and immediately pulled Tony into a hug. After a few seconds Tony patted him on the back as a signal to release.

“What can I do?” Rhodey asked but Tony only shrugged. “We’ll find him Tones. Don’t worry we’ll get Peter home safe.”

“Uh, guys!” Sam called. “Boss-” Friday interrupted.

Tony jumped up and ran over to where a new video was being live streamed. All of them gasped at the sight. “Your kid’s just like you Stark. Only you escaped on your first try.” Peter was tied to the chair again but instead of rope holding him down it was sharp copper wires digging into his skin. There was also blood dripping down from Peter’s hairline. Peter lifted his head and looked straight into the camera lens. “I’m okay Dad.” Peter’s voice sounded hoarse from crying.

“No he’s not.” A man said as a baseball bat came down hard on Peter’s wrist. Peter cried out in pain. “We’re going to send you a link to deposit the money. You have until midnight. I would also keep in mind what’s going to happen to Peter here if you don’t comply.” The video cut out.

___________

“Hey Happy. It’s been a while.”

**Notes for the Chapter:**

> Sorry it took so long. I hope you like it. I know it was a bit short but chapter three will either be posted later today or tomorrow. Next chapter will have more involvement with the rest of the team. Also I love reading your comments. <3

**Author's Note:**

> I hope you enjoyed the first chapter! Also let's pretend that Flash and Brad are Peter's friends (don't worry Peter will still have a bully to deal with I love angst) they (Peter's friends) will be important later. Next chapter will be up later this week!


End file.
